The chapel, located at Forward Operation Base Orgun-E, became the subject of controversy after an atheist soldier complained and the president of American Atheists sent a letter to the Pentagon.

“Soldiers with minority religious beliefs and atheists often feel like second-class citizens when Christianity is seemingly officially endorsed by their own base,” American Atheists president David Silverman told Fox News. “We are very happy the Pentagon and the Army decided to do the right thing.”

A military spokesman told Fox News the cross was literally dismantled and will be removed from the base to be in “compliance with Army regulations and to avoid any misconception of religious favoritism or disrespect.”

“After a Christian prayer, the cross was removed from the roof of the chapel,” the spokesman said. “During the removal, the cross was dismantled; however the cross was reassembled and currently awaits transportation to a larger operational base.”

The military told Fox News the cross will only be brought out during Christian services and will be designated as a “non-permanent religious symbol.”

Silverman said a Christian chapel on an Army base in Afghanistan could have put American troops in danger.

“It inflames this Muslim versus Christian mentality,” he said. “This is not a Muslim versus Christian war — but if the Army base has a large chapel on it that has been converted to Christian-only, it sends a message that could be interpreted as hostile to Islam.”

An Army spokesman said all chapels must be religiously neutral.

“The primary purpose of making a chapel a neutral, multi-use facility is to accommodate the free exercise of religion for all faith groups using it,” he said. “We take the spiritual fitness of our Soldiers seriously and encourage them to practice their faith and exercise their beliefs however they choose.”

Courtesy of American Atheist

Retired Lt. Gen. Jerry Boykin, of the Family Research Council, told Fox News a Christian cleansing of the military is under way.

“I don’t think you can categorize it any other way,” he said. “There is a strong effort, led partially by the Administration as well as by atheist groups to destroy the identity of who we are as a nation and that means robbing us of our history.”

Boykin said he fears that the attacks on the Christian faith of soldiers could destroy the morale and the readiness of the military.

“In the long term, the greatest casualty of the conflict in Afghanistan is probably going to be the First Amendment rights of the American soldiers and the faith upon which America was founded,” he said. “I’m very concerned what the administration is doing to the military on a number of fronts. This is another indicator of how we are trying to impose a liberal agenda upon the people that are protecting the very rights of all Americans to be able to worship freely.”

“Why are we ashamed of one of the major reasons our Nation is the most generous and self-sacrificing for the benefit of others that the world has ever known – our inherently Christian benevolence,” he told Fox News. “We have freed the oppressed, fed the hungry, and restored nations throughout the world without anything in particular to show for it other than the satisfaction of making the world better than we found it for the sake of goodness and doing the right thing. Why should we hide a major motivation that compels Americans to do this?”

Ron Crews, the executive director of the Chaplain Alliance, told Fox News he was extremely disappointed to hear the news.

“I’m so concerned that the military is caving in to an organization that does not understand the First Amendment,” Crews said. “Christians have every right to exercise their faith in the military.”

Crews said the removal of the Christian symbols was another example of “yielding to an atheist culture that is not represented by the vast majority of our military personnel nor the people who make up this nation.”

“It appears Christianity is being marginalized in our military,” he said. “The fact is Christian military personnel have the right –the God-given, Constitutional right to worship in an environment that speaks of who they are — and that includes having the cross as a symbol in a place of worship — even in a Muslim country.”

Boykin called on Americans to call their elected representatives and make a “vehement protest” against what is taking place.

He said it’s no coincidence the Obama Administration is using the military, a bastion of traditional American values, to implement social changes.

“You are seeing an assault on the military in an effort to change our society,” he said. “The traditional values of the Judeo-Christian beliefs that America was founded upon – is a target of the Administration.”